My Dad's cummins has the FASS fuel system, which should easily replace the stock lift pump. The stock lift pump is leaking, and not really needed. Can we just remove it and plate off the hole to bypass the lift pump entirely?

it might be getting too much pressure from the FASS.
I'd replace the mechanical fuel pump and sell the FASS.
Just me, the mechanical fuel pumps on those are uber reliable, unlike the POS carters on the 24 valve VP(mine).

we're pretty happy with the FASS, it is a nice system. Ended up just replacing the 75 cent o-ring on the pump and she's not leaking anymore. I was weary of plugging the inlet and outlet of the mech pump because it's still "pumping" and wouldnt have anything inside to pump, might get hot, bind up, etc.

The FASS puts out 15psi max fuel pressure, so it shouldn't be affecting the mech lift pump, but who knows.